Comprehensive exploration of the methylome

NGS enhances epigenetic studies with high coverage density and flexibility

Methylation Sequencing

Introduction to Methylation Sequencing

Cytosine methylation can significantly modify temporal and spatial gene expression and chromatin remodeling. Leveraging the power of next-generation sequencing (NGS), both genome-wide analysis and targeted approaches can provide insight into methylation patterns at a single nucleotide level.

Advantages of Methylation Sequencing:

With whole genome bisulfite sequencing, view methylation at practically every cytosine in the genome across most species

Capture full sample diversity with small amounts of DNA

With targeted methylation sequencing, cover emerging regions of interest in the human genome identified by ENCODE, FANTOM5, and the Epigenomics RoadMap Consortium.

Discover methylation patterns of CpG, CHH, and CHG regions across the human genome

Advancing DNA Methylation Studies with NGS

This ebook discusses genomics applications in gene expression and regulation research. See how workflows can impact study results.

Sequence a Sample With No Loss of Information

Many approaches leverage the high quality and sensitivity of NGS for methylation analysis. Most methods rely on bisulfite conversion of DNA to detect unmethylated cytosines. Bisulfite conversion changes unmethylated cytosines to uracil during library preparation. Converted bases are identified (after PCR) as thymine in the sequencing data, and read counts are used to determine the % methylated cytosines.

Bisulfite conversion sequencing can be done with targeted methods such as amplicon methyl-seq, target enrichment, or with whole-genome bisulfite sequencing (WGBS). Additionally, alternative chemistries like OxBS and TAB-Seq can be used with NGS for identification of hydroxymethylation (5-hMc) in conjunction with methylation (5-mc) analysis.

For a deep dive into methylation analysis methods, please see the Field Guide to DNA Methylation Analysis. View Guide.

Whole Genome Methylation Coverage

Methylation Sequencing Workflow

More than 90% of the world’s sequencing data is generated using Illumina NGS technology.*

In addition to industry-leading technology, Illumina offers a fully supported workflow, from library preparation to data analysis, for methylation sequencing.

For WGBS or targeted methylation sequencing. Maps bisulfite-treated sequencing reads to the genome of interest and performs methylation calls using the Bismark algorithm. Bowtie 2, an ultrafast, memory-efficient tool, aligns the reads to long reference sequences.

Methods Guide

Access the information you need—from BeadChips to library preparation for genome, transcriptome, or epigenome studies to sequencer selection, analysis, and support—all in one place. Select the best tools for your lab with our comprehensive guide designed specifically for research applications.

Related Solutions

Epigenetic Changes in Cancer

Studies of epigenetic alterations in cancer, such as aberrant methylation and altered transcription factor binding, can provide insight into important tumorigenic pathways. As altered methylation often activates or silences genes, changes in the epigenome can affect gene expression and the rate of cancer progression. Learn more about cancer epigenetics.

Complex Disease Genomics

Genome-wide methylation profiling can help researchers understand the functional mechanisms at work in complex disease cases. Aberrant cytosine methylation can impact gene expression, and has been implicated in many disease processes, such as Alzheimer’s disease and asthma. Learn more about complex disease research.

Illumina Summary

An essential basis for using Chinese hamster ovary (CHO) cells for producing therapeutic proteins is a well-characterised genomic sequence and transcriptome data and a deeper understanding of genotype–phenotype relationships. This paper presents the first DNA methylation map of a CHO cell line in single base resolution, generated by illumina whole genome bisulfate sequencing combined with gene expression analysis. The authors showed that CHO DP-12 cells exhibit global hypomethylation compared to a majority of mammalian methylomes and hypermethylation of CpG-dense regions at gene promoters called CpG islands.

Changes in epigenetic marks such as DNA methylation and histone modifications are being studied with genome-wide assays to give insight into the epigenome remodelling in cellular differentiation. This study presents a whole-genome bisulfite sequencing (WGBS) assay that enables DNA methylation mapping in very small cell populations and single cells. Illumina sequencing combined with a bioinformatic method for analyzing collections of single-cell methylomes allowed the authors to study single-cell cell-state dynamics. This assay has many potential uses in assaying composite methylomes and cell-to-cell heterogeneity in complex tissue samples.

Induced pluripotent stem cell (iPSC) reprogramming allows somatic cells to be transdifferentiated to other cell types presumably without passing through a pluripotent state. This study examined the method of iPSC reprogramming using genetic lineage tracing for expression of endogenous transcription factors and X chromosome reactivation using Illumina RNA sequencing and whole-genome bisulfite sequencing for DNA methylation. The authors showed that the vast majority of reprogrammed cardiomyocytes or neural stem cells obtained from mouse fibroblasts pass through a transient pluripotent state, and that their derivation is molecularly coupled to iPSC formation mechanisms.

Methylation and Metastasis

At Illumina, our goal is to apply innovative technologies to the analysis of genetic variation and function, making studies possible that were not even imaginable just a few years ago. It is mission critical for us to deliver innovative, flexible, and scalable solutions to meet the needs of our customers. As a global company that places high value on collaborative interactions, rapid delivery of solutions, and providing the highest level of quality, we strive to meet this challenge. Illumina innovative sequencing and array technologies are fueling groundbreaking advancements in life science research, translational and consumer genomics, and molecular diagnostics.

For Research Use Only. Not for use in diagnostic procedures (except as specifically noted).